I changed the timeout to 1 (for testing purposes) I republished the e-spaces that contains my screens and my theme from service center and republished the standard e-space "users" from service center. However I won't logout after 1 minute.

I made sure I didn't checked to remember the login information while logging in. And checked that there where no ajax requests (or any request) going to the server using fiddler (http traffic monitor).

Could anyone tell me what i could be doing wrong?

My best guess would be that this is because the login session is kept within "(system)". Problem is I can't add a configuration or republish (system)

If you need to increase the session timeout for your entire application landscape, that seems not the way to go :). Just adjust the timeout in IIS (see e.g. here), restart IIS (iisreset) and it should work.